The Pechora is the greatest river of the European Russian Arctic, flowing into the Barents Sea. Its estuarine area includes a vast delta, represented by extensive lowlands that are dissected by the complicated network of arms and branches. Despite the Pechora Delta is considered to be microtidal, tides with a range of 0.5–1 m during the low water period have a significant impact on the nature of currents in the main branches and the distribution of runoff among them during the tidal cycle. Tidal sea level fluctuations as well as storm surges determine the reversing pattern of currents over a significant extent of the delta branches. The modern field equipment combined with 2D hydrodynamic modeling has allowed to understand the contemporary flow features and evaluate their possible alterations under climate changes. The climate impact under considered scenarios is more pronounced during the low flow period, and this can lead to the propagation of tidal currents and an increase in water levels in the city of Naryan-Mar (100 km upstream from the mouth). From a flood risk perspective, sea level rise can be offset by a reduction in flood runoff.