Ria Formosa Lagoon is the most important bivalve production region of the South Portuguese coast. However, the microbial contamination has been increasing in the northwest area of the lagoon. This study assesses the microbiological contamination of clams Ruditapes decussatus from the most contaminated area for 1 year period. Escherichia coli levels were weekly determined and related with variations in several environmental parameters: precipitation, atmospheric temperature, solar radiation, wind velocity, humidity and tide height. Highest E. coli levels in clams were associated with periods of heaviest rainfall and lowest temperature, mainly due to diffuse sources of faecal discharges. A seasonal trend was observed: microbial contamination in clams was lowest in summer, with highest temperatures, intense solar radiation and dry weather and higher in the remaining seasons, especially in winter due to the runoff of faecal contaminated waters. Several measurements not only to protect the quality of the lagoon, but also to protect public health were recommended. The most imperative will be to detect and extinguish the diffuse contamination sources. Otherwise it might be necessary to implement an interdiction period of bivalve harvesting after heavy rainfalls.