In this paper, we study the geometry of various Hessenberg varieties in type A, as well as families thereof. Our main results are as follows. We find explicit and computationally convenient generators for the local defining ideals of indecomposable regular nilpotent Hessenberg varieties, allowing us to conclude that all regular nilpotent Hessenberg varieties are local complete intersections. We also show that certain flat families of Hessenberg varieties, whose generic fibers are regular semisimple Hessenberg varieties and whose special fiber is a regular nilpotent Hessenberg variety, have reduced fibres. In the second half of the paper we present several applications of these results. First, we construct certain flags of subvarieties of a regular nilpotent Hessenberg variety, obtained by intersecting with Schubert varieties, with well-behaved geometric properties. Second, we give a computationally effective formula for the degree of a regular nilpotent Hessenberg variety with respect to a Plücker embedding. Third, we explicitly compute some Newton-Okounkov bodies of the two-dimensional Peterson variety.