The polar shelf zones are highly dynamic and diverse systems. In the Arctic shelf region multiple river deltas accumulate organic carbon. They host a unique and very diverse northern fauna and flora. One of the final goals of my work is following ecosystem dynamic of Lena Delta region, Laptev Sea. In framework of this purpose the main task is to tune a basic numerical model which is able to reproduce the climatic changes in the region and to estimate the variability of the climate system. To design appropriate model we are using Finite Volume Coastal Ocean Model. FVCOM is a prognostic, unstructured-grid, finitevolume, free-surface, 3-D primitive equation coastal ocean circulation model developed by UMASSD-WHOI joint efforts. The main objective of current research is to verify the model and analyze temperature and salinity local pattern of mixed layer (up to 50 meters) in the Lena Delta Region of Laptev Sea in a short period of time (less than half a year). Also assess the degree of influence the Lena River runoff temperature, local wind pattern and tides dynamics to temperature and salinity variability in the considered area. The particular attention is paid to assessment of impact local bathymetry data to temperature and salinity local pattern. The calculation processes were carried out on the basis of FVCOM. We used high quality unstructured grid, which allows to take into account complexity of coastline, characteristics of the bathymetry data and features of the problem (the necessity to reduce the size of elements on a main ways of Lena fresh water plumb). Elements sizes are vary from 400m to 3 km. The model contains 6 vertical sigma-layers with 250000 nodes on each of them. The input data (bathymetry and coastline data, atmospheric forcing, temperature and salinity fields for first time step for every depth layer, temperature and salinity on the open boundary nodes for nudging, runoff date) are taken from NOAA, GEBCO, from German and Russian Institutes.