Submarine inflow of freshwater from land into the ocean, (fresh) submarine groundwater discharge (SGD), is increasingly recognized as an important source of local nutrient and pollutants influx to coastal ecosystems. Still, very little is known about the effects of SGD on ecosystem functioning. Especially the effects of fresh SGD on the productivity of higher trophic levels such as ichthyofaunal communities remain unclear. We recorded nutrient, radon, and chlorophyll concentrations and benthic composition in two tropical coral reef lagoons on Mauritius, one influenced by distinctive freshwater springs inside the lagoon (Trou aux Biches) and one influenced by freshwater seepage along the shoreline (Flic en Flac). In Trou aux Biches we additionally examined the load of total suspended solids (TSS) in the water column and recorded and analyzed fish abundance and fish community across nine different stations within three different sites (spring, spring influenced, and control) of the lagoon. Depth measurements were taken using a handheld depth sounder (Plastimo Echotest 2) without consideration of benthic cover. Actual depth might be underestimated, especially in coral rich areas of the lagoon. Water samples for nutrient analysis were taken from a depth of 50 cm using a peristaltic pump, filtered, and stored frozen until measurement. Conductivity, Temperature, and Salinity were measured in situ using a handheld probe (WTW Cond 3310, TetraCon325). Water pH was determined in the laboratory using a stationary pH probe (Ohaus Starter 2100). Additionally, water samples were obtained from two oceanic stations offshore the SGD influenced and control part of the lagoon. Nutrient concentrations were determined using standard methods with a discrete analyzer (Systea Easychem Plus) equipped with a 5 cm absorbance reading unit. 222Rn concentrations were determined using an electronic radon detector (RAD 7, Durridge Co.). Benthic coverage was determined using 50 m point intersect transects. All transects were video recorded (Canon Powershot G16) for subsequent analysis. Transect videos were evaluated in the laboratory, recording benthic makeup every 50 cm (n=100) using classifications by English, Wilkinson, & Baker (1997). Total suspended solids (TSS) were sampled in triplicates along 100 m horizontal transects at the springs, the spring influenced part of the lagoon, and at the control site using a 20 µm plankton net. Per transect,a total of 4.91 m³ water (net diameter 25 cm) were filtered. All samples were kept cold in a portable cooling box and frozen at -20°C in the laboratory for subsequent analyses. Frozen TSS samples were defrosted, filtered on a pre-weighted microfiber filter (Whatman GF/F), dried, and weighed again. For Chlorophyll a determination, 1 liter of seawater were taken from a depth of 50cm, filled into a dark PVP bottle and stored in a portable cooling box. In the laboratory the water was filtered onto a microfibre filter (Whatman GF/F), wrapped in tinfoil, stored at -20°C, and shipped to the ZMT in Bremen, Germany. At the laboratory in Bremen, filters where bisected and one half was used to extract Chlorophyll a, using 96% Ethanol. The Chlorophyll a / Ethanol solutions were measured using a fluorometer (TD10AU Flouru, Ex436, Em680). To evaluate fish abundances, GoPro Hero 4 video cameras were weighted and placed at two stations close to the springs, and at three stations at the spring influenced site as well as at the control site. Video data was evaluated using the MaxN/MIN count method (Cappo et al., 2003). Furthermore, videos were used to a) compose a list of all fish species occurring in the lagoon and b) determinate abundances. Diversity was determined using three commonly used metrics, species richness, Shannon's diversity index H', and Pielou evenness J'. Functional groups were used to evaluate changes in the fish community structuring. Groupings are based on similar ecosystem functioning disregarding taxonomic relationships (Bellwood et al., 2004). Fish species were classified into feeding groups indicating feeding behavior and dietary composition (Pratchett et al., 2011). Herbivores and corallivores were further classified using definitions by Green & Bellwood (2009) and Cole et al. (2008), respectively. Commercial species were determined using an open-source dataset provided by the Mauritius Oceanography Institute (Curpen et al., 2013).