Bija literally means seed, and is used in the same sense in different contexts.
In case of plants it means the seed.
In cosmology it means the seed of creation.
In human context bija is the male principle of procreation. The female principle is called kshetra.
In the science of sound Bija is a word-root, a composition of syllables. It is from these word-roots that the tree of entire language sprouts. In Mantra Sastra the beejas are called Mantra Bijas or Bijaksharas.
Sa-bija and nir-beeja are two forms of meditation, in the first case there is a seed-thought (or word) for meditation and in the second there is none.