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Dreissena polymorpha (zebra mussel) and Margaritifera margaritifera (pearl mussel) are freshwater bivalves. Both are found within the Neagh Bann Catchment in Northern Ireland UK. This project investigated the presence and abundance of D. polymorpha in Lough Neagh, the Lower Bann and Ballinrees reservoir. Whilst D. polymorpha has extended its previously known geographic range in the Neagh Bann catchment beyond the lough, the abundance of this notoriously invasive species has remained very low in Lough Neagh. Inhibiting factors were identified and investigated. Of particular importance was substrate suitability, as 85% of the lough bed is unsuitable for D. polymorpha settlement. Due to Lough Neagh's shallow depth and large surface area wind driven currents frequently resuspend particulate matter which inhibit mussel filter feeding and potentially smother sessile mussels. Water temperature, dissolved oxygen content and electrical conductivity of Lough Neagh did not exceed the tolerance range for D. polymorpha survival and replication. The abundance of the parasitic ciliate Conchophthirus acuminatus in D. polymorpha mussels was compared across Lough Erne, Lough Neagh, the Lower River Bann and Ballinrees Reservoir. The parasite presence/absence pattern suggested that the mussels arrived in Lough Neagh as adults and spread from there as larvae throughout the Neagh Bann catchment. DNA analysis of D. polymorpha from the same four sites provided no evidence for introductions from source areas with genetically different mussel strains. Salmonid fish from the Ballinderry River (Northern Ireland) were exposed to glochidiosis by freshwater pearl mussels (Margaritifera margaritifera) under semi-natural hatchery conditions. Genetically distinct pearl mussel populations from the upper and lower regions of the Ballinderry river both displayed glochidial host preference for river trout (Salmo trutta), notably Dollaghan, thus emphasising the importance of these endemic fish for the future survival of M. margaritifera within the Ballinderry River. No Ballinderry River pearl mussel glochidia survived the parasitic life stage on Atlantic Salmon (Salmo trutta) gills showed that older fish (1+ and 2+) carried greater encysted loads, although they were less susceptible to glochidial encystment than juvenile (0+) fish. Based on other studies glochidia excyst around day 350, in this study by day 337 all glochidia had excysted from host fish during captive bred trials. Margaritifera margaritifera glochidial fish host preference in the Ballinderry River for trout differs from host preference or other pearl mussel populations in Northern Ireland. It is therefore essential that fisheries management policy change conducts risk assessments at a catchment scale, in order to make good conversation and policy choices. An increasing frequency in the occurrence of bacterial multidrug resistance against antibiotics has raised the question about the potential contribution of environmental processed to this rise. In this study's laboratory experiments filter feeding by D. polymorpha had an effect on vancomycin resistance transfer in Enterococcus faecalis. Furthermore, the presence of phytoplankton (Palmellopsis sp.) facilitated higher transfer efficiencies. Presumed conjugal transfer of antimicrobial resistance in D. polymorpha occurred at a maximal transfer efficiency of 10-6. This is evidence for the ability of benthic filter feeders such as D. polymorpha to facilitate the emergence and spread of multidrug resistance against antibiotics among faecal bacteria in aquatic environments which receive pollutant transfers from faecal sources. Careful management of the Neagh Bann Catchment is required to limit the spread of invasive zebra mussels, to encourage the survival and recovery of pear mussel populations through good habitat management and host survival and to minimise the spread of antimicrobial resistance in the natural environment by improved waste and wastewater management.