Whilst there have been many studies indicating links between anthropogenic contaminants and reproductive abnormalities in wildlife, very few studies have addressed the effects that might be occurring at the population level. In this study we aimed to assess the mid and long-term population effects of different levels of intersexuality in an amphipod species, Echinogammarus marinus. This aim was achieved by modelling the dynamics of a population of E. marinus with possible contaminant or parasite induced intersexuality over a ten-year period. The model considers five population groups: juveniles, males, immature females, adult normal females and adult intersex females. The costs associated with intersexuality in E. marinus were incorporated into the model using data from previous studies. The basic run of the model considers a population with 50% normal males and 50% normal females, which are prevalent in some field populations of E. marinus. Results of increasing proportions of intersex females were compared with the basic run and suggest that if intersex females occur at the expense of normal females, the population collapses after approximately 6 and 2.3 years when intersex females account for 5 and 10% of the population, respectively. Conversely, the population density increases exponentially if intersex females occur at the expense of males. However, if the number of intersex females reaches approximately ½ of the number of normal females, even if the percent of males in the population is as low as 27% (e.g. 27% males, 45% normal females, 28% intersex females), the population will be extinguished within 10 years. These results suggest a selective advantage in female-biased sex ratios in populations with significant levels of intersexuality, up to a certain threshold, where the increase in the total number of females seems to compensate the lower recruitment rates of intersex individuals, namely, intersex females. Furthermore, even in this scenario, if the recruitment rate of normal females is negatively affected, the population survivorship may be compromised. Modelling the effects of intersexuality in this manner should aid both environmental toxicologists and ecologists in predicting the population level effects of endocrine disrupting chemicals and/or parasites.