Upcoming projects such as Euclid, LSST, and DESI will measure positions and shapes for hundreds of millions of galaxies, enabling us to probe fundamental physics with weak lensing and clustering analyses at an unprecedented level of precision. However, in this new regime, several astrophysical effects must be understood to ensure that we draw accurate conclusions. I will discuss two effects that can impact observed correlations on cosmological scales: intrinsic alignments (the shapes and orientations of galaxies) and biasing from streaming baryon velocities. Although seemingly separate topics, similar frameworks can be used to study both. Beyond their impact on accurate cosmology, these effects may provide new windows into both fundamental physics and complex astrophysical processes.