Pekalongan River has two functions, i.e., as fishing boat transportation and the main drainage of Pekalongan City. The Pekalongan river estuary has a Jetty located on two sides of the river mouth. The jetty is used to protect from waves and sediment. The Pekalongan river has upstream flow from Kupang and Banger river. Because of the flood incident around 2003, Since 2014, the two rivers became two estuaries. The condition caused a negative impact on sediment in the river mouth. Therefore, this research aims to find solutions by simulating waves, currents, and sediments. In this paper, the focus is on the wave simulation. This research method begins with the collection of primary data in the form of bathymetry measurements at the river mouth. While the secondary data is wind data for 13 years and tidal. Calculation of wind hindcasting figures out a wave at a significantly high value of 1.38 m and a significant period of 4.80 seconds. For wave simulations, it used SMS software in the CGWAVE module. The simulation compares the two jetties condition, in existing and development conditions. Based on the simulation, the wave is still high for existing conditions and becoming low by an extended jetty of 200 m lengths. The simulation results can be used to analyze the movement of sediment transport that is affected by the movement of waves around the river mouth.