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 prove that the resulting second-kind Fredholm integral equations are invertible. In the velocity potential formulation, invertibility is achieved after a physically motivated finite-rank correction. The integral equations for the two methods are closely related, one being the adjoint of the other after modifying it to evaluate the layer potentials on the opposite side of each interface. In addition to a background flow, both formulations allow for circulation around each obstacle, which leads to multiple-valued velocity potentials but single-valued stream functions. The proposed boundary integral methods are compatible with graph-based or angle-arclength parameterizations of the free surface. In the latter case, we show how to avoid curve reconstruction errors in interior Runge-Kutta stages due to incompatibility of the angle-arclength representation with spatial periodicity. The proposed methods are used to study gravity-capillary waves generated by flow over three elliptical obstacles with different choices of the circulation parameters. In each case, the free surface forms a structure resembling a Crapper wave that narrows and eventually self intersects in a splash singularity.
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