It is often said that control and estimation problems are in duality. Recently, in (Aubin-Frankowski,2021), we found new reproducing kernels in Linear-Quadratic optimal control by focusing on the Hilbert space of controlled trajectories, allowing for a convenient handling of state constraints and meeting points. We now extend this viewpoint to estimation problems where it is known that kernels are the covariances of stochastic processes. Here, the Markovian Gaussian processes stem from the linear stochastic differential equations describing the continuous-time dynamics and observations. Taking extensive care to require minimal invertibility requirements on the operators, we give novel explicit formulas for these covariances. We also determine their reproducing kernel Hilbert spaces, stressing the symmetries between a space of forward-time trajectories and a space of backward-time information vectors. The two spaces play an analogue role for filtering to Sobolev spaces in variational analysis, and allow to recover the Kalman estimate through a direct variational argument. For comparison, we then recover the Kalman filter and smoother formulas through more classical arguments based on the innovation process. Extension to discrete-time observations or infinite-dimensional state, tough technical, would be straightforward.