The development of accurate methods to detect and enumerate viruses is an important issue in aquatic microbial ecology. In particular, viruses attached to floating aggregates are a largely ignored field both in marine and inland water ecology. Data on the total abundance and the colonization of aggregates by viruses are rare, mainly due to methodological difficulties. In the present study, we used confocal laser scanning microscopy (CLSM) to resolve fluorescence signals of single viruses and bacterial cells in a complex three-dimensional matrix of riverine aggregates. CLSM in combination with different fluorochromes is a very promising approach for obtaining information both on the aggregate architecture and on the spatial distribution of viruses attached to fully hydrated aggregates. Aggregates from the Danube River harbored up to 5.39 x 10(9) viruses cm(-3). We discuss the problems associated with different methods such as sonication or directly counting viruses on aggregates, both combined with epifluorescence microscopy and CLSM, to quantify viruses on suspended particles.