It is possible that early in the Mesozoic era, lasting from 248.2 Ma (million years) to 65 Ma BP (before present), all the major landmasses were connected into Pangea, though the basal rocks of the Indian peninsula may already have been exposed, as evidenced by land fossils dating back to the Carboniferous period (320 to 286 Ma BP). This land mass probably split into a northern Laurasia and a southern Gondwana early in the Cretaceous period (144.2 to 65 Ma BP); the Indian peninsula bears dinosaur fossils dating back to this period (about 98 Ma BP). The southern land mass also split and the southern part of India started to float towards the Asian plate. The northern part of what is now India was still submerged: Rajasthan and Kucch regions contain oceanic fossils dating back to the Jurassic period (about 213 to 144 Ma BP), and the Himalyan region shows only aquatic fossils till the end of Mesozoic.
On the boundary between Cretaceous and Tertiary periods (65 Ma to 1.64 Ma BP), the Deccan traps, huge lava flows all over the peninsula, were formed. During the transition between the Oligocene (35.4 Ma to 23.3 Ma) and Miocene (23.3 Ma to 5.2 Ma), the Himalayas started rising at the southern edge of the northern Ankaraland plate. The region between the peninsula and the Himalayas was the 2–6,000 meter deep Tethys sea which slowly got filled with silt from the preexisting rivers, and during the Pleistocene (1.8 Ma to 10 Ka) formed the Indus-Ganges-Brahamaputra plain.
Since that period, India has probably occupied the same latitudes, and hence a similar climate, except, of course, due to the vagaries of the global climactic conditions. During the ice age, the Himalayan snowline was probably down to 1800 meters instead of the current 4000 meters above sea level, and even in later Pleistocene, the sea level was probably 100 to 150 meters lower than what it is today, easily connecting all of Andamans into one island, and connecting the Ceylonese island to India. On the other hand during the interglacials, around 120 Ka and 30 Ka BP, the sea level might have been higher than now.
Before the anthropogenic changes in the Indian subcontinent, it is reasonable to expect that the monsoon weather created a combination of eastern wet evergreen forests and western moist deciduous regions. The modern desert regions were also probably more humid, and probably the current tropical thorn forested regions were then still tropical deciduous, and the elephant roamed free from Assam to the western reaches of Mehrgarh. The forested terrain also supported abundant wildlife: the Pleistocene saw seventeen varieties of Indian elephants, and during this phase Hippopotamos inhabited both the Gangetic and the Narmada basins. Even 8000 years back, the Ostrich survived on the Indian subcontinent.
The river systems of the northern plains have shown some change during this period: the existence of the Gangetic dolphin in both the Ganges and Indus basins is evidence for either the Yamuna flowing into the Indus (instead of into the Ganges) or of the Sutlej (shatadru) flowing into the Yamuna instead of being part of the Indus system; sometime in the last million years. Similarly, a huge river system, the Saraswati system, probably flowed into the Indus system and dried up, starting long before humans came here, but continued slowly as the desert formed in the Indian west.