Female-limited polymorphism occurs in different animal taxa but is particularly abundant among species of damselflies (Insecta: Odonata), most likely as a consequence of selection to avoid excessive male harassment. Recent work on the damselfly Nehalennia irene indicated that within year spatial variation in female morph frequencies was limited in nearby populations (i.e. intra-regional scale), but large at a continental scale. As anticipated, some of the observed variation in morph frequency was correlated with variation in the estimated degree of male harassment towards female morphs, measured by male density and operational sex ratio. Here, we extended earlier work by quantifying variation in morph frequency over two to three years, allowing us to elucidate how morph frequencies vary temporally at both intra-regional and continental scales (data for 8 populations over three years and for 33 populations over two years, respectively). Annual variation in morph frequencies was relatively high at the intra-regional scale, but was never large enough to obscure the underlying spatial pattern at the continental scale. At both geographic scales, male density and operational sex ratio were highly variable between years. The estimated degree of male harassment correlated with variation in morph frequency within some regions, but not all. Together, the observed natural variation in female morph frequencies may be partly explained by variation in male harassment, but it appears that a complete understanding will require considering the role of other environmental factors.