Despite peri-urban areas being crucial for ecosystem service provisioning, they usually become degraded, as they are burdened with effluents from urban production activities. Such is the case of Laspias River (Thrace, Greece), where a series of diffuse and point pollution sources are met throughout its course, neglecting the fact that it discharges into a protected area. In an attempt to assist possible management implications in this less-researched river, two years of investigative monitoring provided the insight to test the effect of abiotic parameters in the benthic invertebrate biota and water quality, in turn. The results revealed an avalanche of pressures, where nutrients and organic pollution loads diminish richness and biodiversity, losing any temporal or seasonal pattern, resulting in biotic (taxonomic/functional) homogenization. The river is at a tipping point, and tailored measures must be designed and implemented immediately.