Viral community structure and dynamics were investigated for the first time in surface waters (0–20 m) of Lake Geneva over a 5-month period between July and November 2011. Abundances of autotrophic picoplankton, heterotrophic bacteria and virus-like particles determined using flow cytometry revealed their predominance during the summer months followed by a slight decrease in fall. Two groups of viruses could be discriminated, referred to as virus-like particles (VLP) group 1 and 2. The abundance of VLP1 correlated significantly with the bacterial abundance, while that of VLP2 correlated with both chlorophyll a and picocyanobacterial abundance suggesting a tight coupling between these viral groups and bacteria or phytoplankton. The abundance of cyanomyoviruses and cyanopodoviruses varied between 7.3 × 102 ml−1 (July) to 1.2 × 104 ml−1 (November) and 5.8 × 103 ml−1 (July) to 2.2 × 104 ml−1 (September), respectively. The abundance of the picocyanobacterial hosts was in concurrence with that of the cyanophages, being higher in late summer. Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) of viral signature genes such as g20, g23, mcp, polB, psbA and psbD revealed a relatively high richness within these genes with their diversity increasing towards the summer months. The diversity of psbD was found to be particularly high and correlated with picocyanobacterial abundance suggesting that cyanophages may be directly responsible for a significant proportion of carbon fixation in Lake Geneva.