We present two accurate and efficient algorithms for solving the incompressible, irrotational Euler equations with a free surface in two dimensions with background flow over a periodic, multiply-connected fluid domain that includes stationary obstacles and variable bottom topography. One approach is formulated in terms of the surface velocity potential while the other evolves the vortex sheet strength. Both methods employ layer potentials in the form of periodized Cauchy integrals to compute the normal velocity of the free surface. We also propose a new algorithm to dynamically vary the spacing of gridpoints on the free surface to efficiently resolve regions of high curvature as they develop. We study singularity formation and capillary effects and compare our numerical results with lab experiments.