An investigation into bryophyte communities in karst Jankovac Stream (Papuk Nature Park, Croatia) was carried out once a month from July 2008 to June 2009. Samples were taken from two lotic microhabitats: (i) Jankovac Spring (JS), a hypocrenal habitat with dense bryophyte clusters (90% bottom cover) and (ii) Jankovac Waterfall (JW), with scattered bryophyte clusters (50% bottom cover). At the same time, seston samples were collected during the spring as the source site and after the JW, as the outflow site. The goals of this study were to understand the (i) algal, protozoan and metazoan bryophyte community assemblages in these two lotic microhabitats, (ii) influence of environmental factors on the structuring of the bryophyte community and (iii) structure of seston along the longitudinal profile. A total of 172 taxa were determined: 68 algae, 55 protozoa, 24 meiofauna and 25 macroinvertebrates. Statistically significant differences between two microhabitats differing in percentage of bryophyte cover were established testing 13 environmental parameters. In dense bryophyte clusters, community structure was determined by flow velocity and pH, and macroinvertebrates achieved higher diversity and abundance. On the contrary, in scattered bryophyte coverage algae, protozoa and meiofauna reached higher abundance and diversity governed by the amount of suspended organic matter and epiphyton. In contrast to previous studies, the inverse ratio of community diversity and abundance versus percentage of bryophyte cover was established. We assume this to be the result of an enrichment of the scattered bryophyte clusters by upstream seston. Additionally, the effects of anthropogenic hydromorphological disturbance are reflected in macroinvertebrate diversity and abundance reduction.