Salinity of water sources is a worldwide problem. Desalinization technologies improve the water quality but produce a highly saline residual waste. One proposed method of disposal is transfer into septic systems. We investigated the microbiological response of septic wastewater to saline backwash. Salinity concentration within the range of residual saline waters in the region was included. Diversity of bacteria and fungi was determined using 454-pyrosequencing. Treatments shared a very similar distribution and richness of bacterial and fungal diversity. Fungal diversity was represented mostly by Dothideomycetes members; Pezizomycetes were inhibited with treatment. Operational taxonomic units from Gammaproteobacteria were common throughout treatments and wastewater control, but increased with treatment. Bacterial populations underwent selection with salinity treatment, likely a statistically significant effect (p = 0.06). The study shows that microbial populations in wastewater are an important aspect to consider when introducing brackish waste into waste stream even in these short-term field conditions.