This paper introduces a novel nonparametric framework for data imputation, coined multilinear kernel regression and imputation via the manifold assumption (MultiL-KRIM). Motivated by manifold learning, MultiL-KRIM models data features as a point cloud located in or close to a user-unknown smooth manifold embedded in a reproducing kernel Hilbert space. Unlike typical manifold-learning routes, which seek low-dimensional patterns via regularizers based on graph-Laplacian matrices, MultiL-KRIM builds instead on the intuitive concept of tangent spaces to manifolds and incorporates collaboration among point-cloud neighbors (regressors) directly into the data modeling term of the loss function. Multiple kernel functions are allowed to offer robustness and rich approximation properties, while multiple matrix factors offer low-rank modeling, integrate dimensionality reduction, and streamline computations with no need of training data. Two important application domains showcase the functionality of MultiL-KRIM: time-varying graph-signal (TVGS) recovery, and reconstruction of highly accelerated dynamic-magnetic-resonance-imaging (dMRI) data. Extensive numerical tests on real and synthetic data demonstrate MultiL-KRIM's remarkable speedups over its predecessors, and outperformance over prevalent "shallow" data-imputation techniques, with a more intuitive and explainable pipeline than deep-image-prior methods.