Herein we investigated the cellular responses of the endemic fish species Alburnus vistonicus Freyhof & Kottelat, 2007, under the variation of several physico-chemical parameters including temperature (°C), salinity (psu), dissolved oxygen (mg/L), pH and conductivity (μS/cm), which were measured in situ. Monthly fish samplings (October 2014–September 2015) were conducted in Vistonis Lake in northern Greece, a peculiar ecosystem with brackish waters in its southern part and high salinity fluctuations in its northern part. Fish gills and liver responses to the changes of the physico-chemical parameters were tested biochemically and histologically. Heat shock protein levels appeared to be correlated with salinity fluctuations, indicating the adaptation of A. vistonicus to the particular environment. The latter is also enhanced by increased Na⁺-K⁺ ATPase levels, in response to salinity increase during summer. The highest mitogen activated protein kinases phosphorylation levels were observed along with the maximum mean salinity values. A variety of histological lesions were also detected in the majority of the gill samples, without however securing salinity as the sole stress factor. A. vistonicus cellular stress responses are versatile and shifting according to the examined tissue, biomarker and season, in order for this species to adapt to its shifting habitat.