Spatial and temporal complexities of reproductive behaviour and sex ratios of two harpacticoid species Canuella perplexa Scott T. & Scott A., 1893 and Bryocamptus sp. were evaluated monthly from September 2007 to August 2008. Collections were made from four ponds at different salinities in the solar saltern of Sfax, Tunisia, considering other environmental features as well. The salinities ranged from 38.0 to 86.1 psu. With rising salinity, the abundance of C. perplexa adults declined from 4550 ± 4160 ind m−3 (pond A1, salinity = 41.5 ± 2.3 psu) to 880 ± 780 ind m−3 (pond C31, salinity = 71.0 ± 4.3 psu). The abundance of Bryocamptus sp. adults increased from 3560 ± 2810 ind m−3 (A1) to 10,080 ± 6890 ind m−3 (C31). The abundance of total adults of C. perplexa was negatively correlated with both salinity (r = − 0.441, n = 18, p < 0.05) and abundance of dinoflagellates (r = − 0.291, n = 18, p < 0.05) and positively correlated with suspended matter (r = 0.389, n = 18, p < 0.05), temperature (r = 0.354, n = 18, p < 0.05), and abundance of diatoms (r = 0.410, n = 18, p < 0.05). The abundance of adults of Bryocamptus sp. displayed only a positive correlation with salinity (r = 0.452, n = 18, p < 0.05). In both species, the sex ratio (males/females) was driven by the variability of female abundance but never exceeded 1.0. For C. perplexa, the egg number per female ranged between 28 and 31; the ovisac length was between 0.39 ± 0.002 and 0.45 ± 0.018 mm. The egg diameter ranged from 0.062 ± 0.001 to 0.065 ± 0.002 mm, and the total length of ovigerous females ranged between 1.2 and 1.35 mm. For Bryocamptus sp., the egg number per female ranged between 19 and 22, the ovisac length between 0.28 ± 0.008 and 0.31 ± 0.003 mm, the egg diameter between 0.041 ± 0.001 and 0.044 ± 0.001 mm, and the total length of ovigerous females between 0.6 and 0.74 mm. The outcome of this study demonstrated that under extreme environmental conditions and increasing salinity the percentage of diatoms and dinoflagellates was found to be an essential factor in controlling the abundance and reproduction traits of both harpacticoids in this study. Furthermore, the sex ratios in these harpacticoid populations are complex as many factors can influence and alter the sex ratios in natural populations.