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Seasonal observations of prevalence and intensity of microsporidians and gregarines infecting the native amphipod Gammarus pulex, in the tributary of small Baltic coastal river were analyzed. Using aggregate data from 12 date-by-site comparisons, we found that both prevalence and intensity of Apicomplexa were seasonally unimodal. Parasitism first increased and then declined seasonally after peaking midseason. In the case of infections caused by Microsporidia, the highest increase falls in the early autumn period, reaching the value from 48 to 56%. The minimum share of infected hosts was recorded in March 2016 and January 2017. In the early spring period, there was a slight decrease in microsporidian infection with subsequent minor fluctuations in the summer. We showed that this parasite can decreases the survival of G. pulex in the late stages of infection development in autumn. However, the host reproduction in the spring and the summer could potentially reduce the negative impact of the parasite on host populations.