Presence of pathogenic bacterial pollution in coastal marine environments around the world raises environmental and public health concerns for many reasons, among them due to the potential to spread antibiotic resistance. Wastewater effluents are a major concern, and leachate (run-off) from agricultural areas and animal farms also contribute to this environmental issue. This case study was performed near a recreational beach, Bore beach (Klepp, Norway), to identify the contribution of two potential sources (wastewater effluent 1 km offshore and a stream delivering run-off from an agricultural area) to the coliforms detected by regular monitoring. We performed comparative analysis of the microbial communities present in these sources and their respective recipients along a gradient using 16S amplicon sequencing. In addition, the samples collected at the wastewater effluent recipient point and the treated wastewater were further explored through shotgun metagenomics to obtain insights into the presence of other fecal pollution indicators and into their antibiotic resistance profile. Understanding the exact sources of pathogen pollution near recreational beaches is an essential first step in facilitating the design of targeted water management plans aiming at reducing this type of pollution. The site of this case study, Bore beach, is located on the south-west coast of Norway, in Vestlandet area, which has an over 25,000 km long coastline and has undergone the highest population growth within Norway during the last 10 years. At the same time, the coastline is the focus of a growing and economically important fish farming industry. Therefore maintaining healthy coastal ecosystems and monitoring sources of potentially pathogenic microbial pollutants under such increasing anthropogenic pressure is of great importance for this region.