Pygospio elegans is an opportunistic, wide-spread spionid polychaete that reproduces asexually via fragmentation and can produce benthic and pelagic larvae, hence combining different developmental modes in one species. We documented the density, size distribution, and reproductive activity of P. elegans at four sites in the Danish Isefjord-Roskilde Fjord estuary complex, where all modes of reproduction were reported. We compared population dynamics of this species to environmental parameters such as salinity, temperature, and sediment characteristics (grain size, sorting, porosity, water content, organic content, C/N). We observed that new cohorts—resulting either from sexual or asexual reproduction—appeared in spring and fall, and old ones disappeared in late summer and winter. Sexual reproduction occurred from September until May, and although their timing was variable, there were two reproductive peaks at three sites. At those sites, we also observed a switch in larval developmental mode. Asexual reproduction peaked in April. While the seasonal dynamics can be related to temperature to a large extent, the differences in population dynamics among sites also correlated with sediment structure and salinity. Populations from sites with coarse and heterogeneous sediment had high levels of sexual reproduction. At the site with lower salinity, intermediate and benthic larvae were present during winter in contrast to pelagic larvae found at the other sites. However, we could not identify one clear environmental factor determining the mode of development. At present, it remains unclear to what degree genetic background contributes to mode of development. Hence, whether the differences in developmental mode are the result of genetically different cohorts will be further investigated.