We have studied the behavior of nonlinear waves in isothermal atmospheres using an improved beam scheme method. It is shown that although the magnitude of the mass leakage due to side beams is significant, nevertheless in a motion close to hydrostatic equilibrium it can be suppressed, if special density distributions and/or suitable mesh intervals are selected. We adopt as the parameters for our model of the atmospheresM=1 M⊙,R=50 R⊙ andT=4864 K. The time variation of the physical quantities in each cell is found for several oscillation periods. The critical frequency for the model atmosphere in the case of waves with a weak nonlinearity seems to be consistent with that in the linear theory.