Bivalves are ancient animals that feed by filtering large volumes of water. In this way, phytoplankton, bacteria and viruses from the water column are greatly concentrated in the mussels. The hazards associated with the consumption of mussels are thus dependent on the occurrence and composition of toxic algae and human microbial pathogens in the areas where shellfish are grown. Diarrheic shellfish toxins have occurred regularly in Sweden during the past 27 years. Peaks of toxins in mussels are mostly recorded from October to December, but the pattern can differ significantly due to location and year, making it hard to predict toxin levels in mussels. With an expansion of aquaculture and a subsequent increase in seafood consumption, better risk management is needed to minimize the effects on humans of algal toxins and human pathogens. New control strategies that have to be implemented are: i) proper site selection of culture installations; ii) regular and cost-efficient monitoring of algae, bacteria and viruses; iii) new indicators for fecal contamination, suitable for the specific locations where shellfish grow; iv) rapid dissemination of information to the industry and public, including risk assessment and advice on how to cope with the situation.