We investigate the stationary (late-time) training regime of single- and two-layer linear neural networks within the continuum limit of stochastic gradient descent (SGD) for synthetic Gaussian data. In the case of a single-layer network in the weakly oversampled regime, the spectrum of the noise covariance matrix deviates notably from the Hessian, which can be attributed to the broken detailed balance of SGD dynamics. The weight fluctuations are in this case generally anisotropic, but experience an isotropic loss. For a two-layer network, we obtain the stochastic dynamics of the weights in each layer and analyze the associated stationary covariances. We identify the inter-layer coupling as a new source of anisotropy for the weight fluctuations. In contrast to the single-layer case, the weight fluctuations experience an anisotropic loss, the flatness of which is inversely related to the fluctuation variance. We thereby provide an analytical derivation of the recently observed inverse variance-flatness relation in a deep linear network model.