The island of Mauritius is divided into 25 major river basins and 21 minor ones with catchment areas varying from 3.9 to 173 km². Almost all major rivers are perennial with most of the streams having their sources in the central plateau. The freshwater biodiversity of Mauritius is contained within 92 rivers and 232 rivulets, several manmade reservoirs, natural lakes and marshy areas. The island of Rodrigues has been divided into 20 major river basins and 10 minor ones, which have been for the most part that has dried up.

18 species of fish and 10 crustacean species were recorded in the main rivers of Mauritius according to the survey by  Association Réunionnaise de Développement de l’Aquaculture (ARDA) in 2003 . Three endemic crustacean species were also inventoried: Cardina mauritii, Cardina spathulorostris and Cardina richtersi (petite chevrette). However, most of those species are few in number.

Many of the watercourses in Mauritius become overgrown with invasive plant species have infested about 95 % of riverbanks.  Freshwater resources are threatened by dumping of solid wastes in rivers, heavy use of agrochemicals in nearby agricultural fields, sewage disposal, and backfilling of coastal wetlands.

There are 203 coastal wetlands in Mauritius and Rodrigues. Wetlands are classified as (a) Natural Wetlands such as Coastal Marshland including tidal mudflats located along the coastline, Freshwater Marshland (inland) and Marine Wetlands; (b) Man-made Wetland such as Reservoirs and Dams. Ongoing wetland decline in Mauritius not only contributes to the loss of local biodiversity but reduces the larger ecosystem role these habitats play in regulating surface water and protecting adjacent marine habitats. In Rodrigues, although the mangrove planting programme undertaken since the mid-80’s has met with variable success in the different sites, the general trends show an increase in mangrove. In 2011, Mauritius designated its third Wetland of International Importance (Ramsar Site), the Pointe d’Esny Wetland (22 hectares) in the south-eastern district of Grand Port. Rare species such as Sesuvium ayresii are protected and conserved in the Rivulet Terre Rouge Estuary Bird Sanctuary (RTREBS) found in the north west of the island at Mer Rouge near the village of Roche Bois. The most common migratory birds observed in RTREBS are the common sandpiper, and common tern.

There is not yet any legislation for the protection of wetlands. Development on wetlands warrants an Environmental Impact Assessment (EIA) and Environmentally Sensitive Areas (ESAs) are protected in the Outline Planning Schemes. It is noteworthy that the Draft Environmentally Sensitive Areas Conservation and Management Act submitted as part of the ESA Study proposes a number of uniform rules for the valuation of lands, enforcement of easements, and the development of other types of incentives for conserving and managing ESAs. It was also highlighted that there is no existing management plans for caves, which fall under Wetlands according to the Ramsar Convention.

Mainland Mauritius has a coastline of 322 km and is surrounded by 150 km of protective coral reefs, covering a lagoon area of around 243 km². The coastal zone consists of sandy beaches, coastal dunes, rocky shores, near shore wetlands and mangroves, lagoon corals, fringing coral reefs and all their associated marine life. Mangrove wetlands provide a natural buffer controlling surface water runoff to the lagoon by neutralising pollutants, nutrients and sediments, which might damage the lagoon ecosystem. Two species of mangrove, Rhizophora mucronata and Bruguiera gymnorrhiza grow around Mauritius. Rodrigues has a coral reef platform that forms an almost continuous rim, 90 km long and from 50 to 10,000 metres wide which encloses a lagoon of 240 km².

The algal flora is rich with over 160 genera of marine algae having been identify in coastal waters. Over 36 species of seaweeds have been identified in Mauritian waters, including Enteromorpha, Ulva, Sargassum, Caulerpa spp., Padina and Halimeda. Macrofauna consists of 10 major faunal groups consisting of polychaetes, pelecypods, isopods, ophiuroids, tanaidaceans, amphipods, gatropods, branchiopods, echiurid worms, and sipunculids. Polychaetes are the most important macrobenthic group, followed by peracarid crustaceans and molluscs. Among crustaceans, the isopods are more frequent than either amphipods or tanaidaceans.
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There are 700 species of coral and five types of reef around Mauritius: fringing reefs, patch reefs, atolls, reef flats and barrier reefs. Fringing reefs occur in shallow waters near to land, extending to depths of 15 – 45 meters. Fringing coral reefs encircle Mauritius and protect it from the sea. Patch reefs are found in relatively shallow waters around Mauritius where the underlying seabed has been close enough to the surface for corals to grow. Atolls start as fringing reefs around volcanic islands, forming atolls as the island gradually submerges. The Mauritian offshore islands of the St. Brandon archipelago include a group of 22 atolls. Reef flats are formed as the fringing reef pushes steadily seaward leaving behind limestone areas that are eroded almost flat by the sea. Reef flats do not occur around the island of Mauritius but are significant around Rodrigues. Barrier reefs are usually found far from the main shoreline and are separated from the shore by broad and deep waters. These occur in the south east of the island.

The coral reef habitats around Mauritius and Rodrigues are being degraded. In Mauritius, coastal development, sedimentation, marine pollution, anchor damage and pollution from inland activities are the main drivers of this degradation. In Rodrigues over-fishing, bad fishing practices, climate change, and sediment input are the major threats. The main natural and human-induced threats to coral reefs are tropical cyclones, climate change and predators such as the crown of thorn starfish and drupella snails. For the past few decades, there has been an increase in both extent and severity of bleaching around the island due to warm-water anomalies, which have led to the degradation of the Mauritian reef. Reefs of the Mauritius lagoon have lost more than 50 % – 60 % of their coral cover. Boat anchors and fishing nets are also responsible for localised damage to corals. Reduction in coral reef habitats is posing a serious threat to biological diversity. Safeguarding the reefs is therefore a priority.

Benthic (seabed) fauna
The distribution of benthic fauna in waters around Mauritius has not been extensively studied. However, several species of crabs, shrimps, lobsters, molluscs, octopus and sea cucumbers are abundant and are of commercial value. Four species of crabs and five species of Penaeid shrimps as well as two species of deep-water shrimps have been identified in Mauritius and are currently being fished. Two species of lobsters are fished around Mauritius and St. Brandon. Other marine invertebrates comprise polychaetes, bivalves and isopods. Among other groups, amphipods are important. Among crustaceans, the isopods are more frequent than either amphipods or tanaidaceans.

Fisheries
Out of 340 species of fish, which have been identified in the waters of Mauritius, 42 are of economic importance within the inshore area, with a different composition and relative abundance in the near shore waters of each island within the country. There are 149 commercial fish species, out of which 42 are new records to Mauritius and 3 may be potentially new species based on DNA assessment. The effect of over-fishing of Lethrinids is apparent on the fringing reefs of Mauritius with a population explosion of sea urchins Diadema sp. and Echinometra spp.

Fishery resources have been traditionally exploited in lagoons and offshore areas around Mauritius, Rodrigues, St. Brandon, the Chagos Archipelago and other outer islands. There are four main types of fisheries in Mauritius namely; (i) artisanal fishery; (ii) sport fishery; (iii) banks fishery, and (iv) tuna fisheries. Artisanal fishing provides employment and livelihoods to some 2,200 fishermen and their families. The main families of fish that are caught are Lethrinids, Siganids, mullets, Scarids and groupers. Reef and demersal fish (fish that feed at the bottom of seas or lakes) stocks are over-exploited and no substantial increase in fish production in these areas is expected in future. The total catch of this fishery is estimated at 400 tonnes per year, consisting mainly of bill-fishes and tunas. The banks fishery consisting of mainly Lethrinids (90 %) catches around 3,000 tonnes annually. The tuna fishery is split into the Fish Aggregation Devices (FADs) and the offshore industrial tuna fishery. Tuna and tuna-like species are caught by local fishermen off-lagoon and around FADs. The total landings from FADs and sport fishermen are estimated at around 650 tonnes annually. Species caught are big eye tuna, skipjack, yellow fin tuna, dorado, wahoo and sharks. Industrial tuna fishing is carried out mainly by long-liners and purse-seiners mostly licensed foreign fishing vessels that catch about 10,000 tonnes yearly in the EEZ of Mauritius. The species caught are mainly skipjack tuna and yellow fin tunas. Other fisheries resources include the deep-water shrimp with an estimated Mean Sustainable Yield (MSY) of 200 tonnes. Total fish catch has declined from 19,690 tonnes in 1993 to 5,270 tonnes in 2011. The potential for aquaculture is estimated to be 29,000 tonnes of fish in the medium term and about 39,000 tonnes of fish annually in the long term.

Rodrigues has 493 fish species, 175 gastropod species, 104 species of algae, 109 bivalve species, 138 coral species, 74 species of echinoderms and 41 bryozoan species. For many of the taxa considered, Rodrigues appears to be less diverse with the notable absence of certain species common elsewhere in the area.　For Rodrigues, the total fish catch increased between 2010 and 2013 up to 68 % of which fish caught in the lagoon made up to 94 % while off-lagoon fishing decreased by 19 %. The increase in total fish catch over the last four years may be attributable, in part, to over-fishing in the lagoon and to a significant increase in octopus population as well as their increase in size and weight since 2012. These trends are related to the development of the Marine Reserves in Rodrigues originally identified by the fisher communities and the implementation of regulations on seasonal octopus closure. In parallel to these developments, a sensitisation campaign was launched across the island associated with the development of alternative activities during the closure period to ensure proper understanding of the motivations that led to this management decision.

Marine biodiversity is threatened by habitat destruction, soil runoff and erosion resulting in excess nutrients from fertilizers and domestic sewage, which then leads to harmful algae blooms that can have severe effects on marine life.

The major threats to coastal biodiversity are coastal erosion, which accounts for 45-50 % of the erosion in Mauritius (ICZM, MOSD); coastal development, pollution, natural hazards (storms, cyclones, tidal surges), Exotic and invasive species, climate change (increase in sea temperature), over-fishing Coastal erosion is a crucial issue and contributes substantially to shoreline changes and to exacerbating poverty in coastal zones.

Coastal Development: On Wetlands there are unsustainable patterns of development such as backfilling of wetlands for construction (about 90 % of all wetlands have been destroyed this way), the absence of drains and sewer network are putting pressure on the coastal zone. Some 7 km of beach have been affected by erosion, and are being further degraded by hard structures constructed on the beach. As a result, the natural functions of wetlands, that is water drainage and filtering of toxic substances, have been impaired.

Pollution: Seagrass meadows are eutrophication of nearshore habitats due to domestic and agricultural runoff and throughflow of nutrients from coastal areas, input of terrigenous sediment by erosion and overfishing in the lagoon.

Invasive alien species: In the Mauritius EEZ, no marine invasive species have been recorded in the Global Invasive Species Database but the status of invasive species in the marine environment in Mauritius is poorly known.

Climate change: There are symptoms of climate change in Mauritius:

• Average temperature has increased by 0.74 °C – 1.2 °C (against the 1961-1990 mean);
• Decreasing trend in annual rainfall of 8% over Mauritius since the 1950s;
• Increase in sea level rise of around 5.6 mm/year;
• Beach erosion (loss of about 18,500 m² of beach area over the last 20 years);
• Coral bleaching events (1998, 2009 and 2016);
• Increase in extreme weather events such as stronger cyclones, and heavy rains leading to flash floods such as in 2008 and 2013.

Marine Protected Areas: Marine Protected Areas comprising Fishing Reserves, Marine Parks and Marine Reserves, have been established in the waters around Mauritius and Rodrigues to conserve marine biodiversity. The Republic of Mauritius has proclaimed 6 Fishing Reserves and 2 Marine Parks namely Balaclava (485 ha) and Blue Bay (353 ha) as well as 5 Fisheries Reserved Areas, 4 Marine Reserves (Rivière Banane, Anse aux Anglais, Grand Bassin, Passe Demie) and a multiple-use Marine Protected Area in the south east of Rodrigues (SEMPA). The Blue Bay Marine Park is known for its diverse and rich fauna and flora especially the corals, mainly for a brain coral of diameter 6 – 7 metres. 108 species (33 genera) of coral, 233 fish species, and 201 species of molluscs were inventoried in 2012.

In Rodrigues, the South East Marine Protected Area (SEMPA), gazetted in 2009, is implemented in the Southern part of the Rodrigues lagoon and has been successfully maintained. It covers a sea surface area of about 43 km² stretching from the shoreline to the 20m isobath. It is composed of a variety of habitats including off-lagoon waters, reef slopes, reef flats, channel reefs, back reef areas and seagrass beds. Its area has been sub-divided into several multiple use zones and key planning documents have been drafted for successful management including several studies. SEMPA was designed to be a showcase of participatory MPA management. Important global benefits were generated through the creation of SEMPA and its strengthened management through participatory approaches. A main challenge in SEMPA is the lack of local capacity in MPA management. The 4 Marine Reserves gazetted in 2007, are located in the northern and north-western sectors of lagoon and occupy ~20 km². All four reserves were demarcated in 2009 and 2010; however, all demarcation buoys were lost, due to failure to properly secure them, bad weather and vandalism. A management plan was drafted in 2011 by a Technical Sub-Committee composed of various stakeholders including fishers, NGO officers, tour operators, MPA officers and fisheries protection officers, and compiled by a team of international scientists. The main challenge for the northern reserves is the lack of local capacity and workforce to implement the management plan.

Coral reef protection: The Mauritius Oceanography Institute implemented a pilot coral farming project in 2008 for culturing corals under controlled conditions in land based nurseries. Culture techniques were developed for the ex-situ propagation of various coral species including fast-growing species, bleaching resistant species/strains and threatened species for conservation initiatives and rehabilitation of degraded lagoons of Mauritius. In parallel, scientific monitoring of the marine environment was undertaken for the identification of resilient coral species and of appropriate sites to implement small-scale reef rehabilitation.

Reef rehabilitation is essential to enhance its ecosystem functions such as increased habitat for improved fish and coral recruitment. Hence, for the past six years, fifteen permanent coral reef monitoring stations and an in-situ temperature monitoring network have been established in-shore and off-shore at different sites around the island. As from 2011, a small-scale reef rehabilitation project was implemented by the MOI. Locally adapted multi-layered rope nurseries were set up at Albion, Flic en Flac and eventually at Trou aux Biches in 2013 in collaboration with the NGO, ELI-Africa for in-situ mass propagation of eighteen selected coral species (including fast-growing and bleaching resistant species/strains) prior to transplantation to either locally-adapted artificial reef rehabilitation modules or on natural substrates. Coral fragments were grown in rope nurseries for a period varying from eight to twelve months before their eventual transplantation to selected recipient reef sites. To date, nursery-grown coral colonies from the nurseries have been used to rehabilitate small degraded areas of 350 m², 300 m² and 150 m² at Albion, Flic en Flac and Trou aux Biches respectively.

The Ministry of Fisheries has also been undertaking reef rehabilitation at selected degraded reef sites since 2008. Coral fragments are fixed to coral farming tables which provide at the same time shelter to fish and other marine organisms, acting hence as a self-sustaining marine system. Under the Africa Climate Change Adaptation Programme, the Ministry also acquired a funding of MUR 1.2 million and carried out coral farming at five sites in Mauritius and Rodrigues in 2012.

The second way to rehabilitate coral reefs is via direct restoration of damaged coral habitats, by attaching coral nubbins directly to the substrate using either with nails and cable ties for attachment to limestone pavements, or cable ties for attachment to recently deceased coral colonies. Nubbins are collected from areas suffering severe fragmentation as a result of fisheries related damage to reefs. These two techniques have successfully been applied in Rodrigues within the Anse aux Anglais Marine Reserve and at other northern and eastern lagoon sites. Success rates are above generally above 70%.