Background: Haemodialysis (HD) superimposes additional circulatory stress on the microvasculature, leading to endothelial dysfunction, which plays a key role in the development of haemodialysis-associated multiorgan dysfunction. This study was undertaken to evaluate the effect of a single HD session on retinal and choroidal microcirculation, using optical coherence tomography angiography (OCTA) in relation to changes in the blood levels of selected biochemical modulators of endothelial function. Methods: The vessel density (VD) of 35 patients was evaluated before and after a single HD session, using OCTA in the superficial capillary plexus (SCP), deep capillary plexus (DCP) and choriocapillaris (CC). Retinal thickness (RT) and choroidal thickness (CT) were also assessed. Asymmetric dimethylarginine (ADMA), endothelin-1 (ET-1) and malondialdehyde (MDA) levels, oxidative stress (OS) status and systemic parameters were assessed before and after a single HD session. The correlation between changes in these parameters and changes in selected OCTA parameters was tested. Results: A single HD session resulted in a significant increase in RT and a decrease in CT. In addition to increased oxidative and osmotic stress resulting from a significant reduction in plasma osmolality, the HD session was associated with a significant increase in ET-1 levels and a decrease in ADMA levels. These biochemical changes correlated with changes in RT and CT, as well as with changes in VD in the retinal capillary plexuses and the CC. Increased ET-1 levels and decreased plasma osmolality were identified as predictors of RT increase, whereas increased MDA levels corrected serum creatinine-predicted CT reduction. Conclusions: Changes in ADMA and ET-1 and OS, as well as osmotic stress induced by a single HD session, affect the eye microcirculation and morphology of the retina and choroid. OCTA examination is a promising method for assessing microcirculation in HD patients.