The population growth from the latter half of the 16th century to the late 17th century was very much done through the opening of agricultural lands. New land opened by the felling of forests, reclamation, as well as the improvement of existing land through using of fertilizers and construction of irrigation. The daimyo of course encouraged this, as more production means more taxes. With the end of war means conquest and expansion was not an option. At the same time, there were no more marauding armies and much less disruptive large-scale mobilization and expedition. Certainly, mobilization to build and repair the castle and castle town, roads, irrigations, and running the postal service took a heavy toll on the general population. But at least those men mobilized for such duties were most likely going to come home after a few weeks or month or two of work, and at least some of those works partially or indirectly benefited the general population as well. One of the policies of the daimyo, while applied unevenly, also moved a lot of samurai out of the hair of the local villages (more on this later). For the daimyo, this was good to remove the middle-man so he could tax the population directly, with more up-to-date and detailed land surveys. But for the general population, this meant the village elders were able to figure out by themselves how best to pay the agricultural tax assigned to them, after that the samurai basically left them alone, meaning there were less pressure from local oppressive strongmen and tax farmers. Detailed land-surveys, combined with more detailed laws with regards to things like water usage rights, as well as policies that exempted or temporary decreased taxes for people who opened new lands or improved lands, meant there was a huge drive to open up new lands.

By the 18th century, however, this has basically reached its limits. What land that realistically could be opened up for farming was already opened. Not only that, newly opened land were mostly at higher elevations, in what used to be swamps, and denser forests. These farms were naturally of poorer quality and more sensitive to things like flooding and landslides. Urbanization also naturally meant more population was depended on imported food. Likewise, the accompanying growth in commerce meant a lot of land was dedicated to growing cash crops like cotton, so it wasn't only the cities which depended on importing food from other regions. Not only that, due to the heavy emphasis of growing of rice for tax purposes (tax rice was then distributed to samurai or sold to merchants), many areas which used to grow mostly crop more well adapted to the cold like wheat, millet, or buckwheat, began growing more rice, a crop from warmer climates. During the period of the opening up of new land for agriculture also meant that families were likely to splinter into branches as groups moved off to live on the newly opened farms. When there was land that could still be opened, this was not such a problem. When there wasn't, however, it meant that many farm plots were broken up into smaller plots barely able to support a family unit. Such families were forced to have less children as the farm simply was not able to support more people. Given such circumstances, the Japanese population was incredibly sensitive to adverse events.

And from roughly 1700 until the around the time of the Meiji Restoration, Japan was hit by adverse event after adverse event. Being unfortunately in the middle of the Little Ice Age, combined with major volcanic eruptions in Japan and around the world, this period had three country-wide famines (1730s, 1780s, 1830s) as well as hundreds of local famines. There also seemed to have been more epidemics during this time than before (31 in the 18th vs 16 in the 17th), though widespread malnutrition likely contributed to these outbreaks. There was also a major famine in the 1640s, but given time and room for growth, population quickly recovered and grew above pre-famine levels. But given how specialized and sensitive Japanese society had become by the 18th century, Japan became trapped in a cycle of death, slow recovery, only to be faced with another major dying again, resulting in no net population growth for most of the period.

As for urbanization, what lords experienced in the Sengoku was that giving samurai local autonomy, in the form of land, income, and people, also made them harder to control and order around. As they had their own income and their own band of warriors (how ever small) should something happen they were likely to try to weasel out of levy responsibilities, ignore orders, or even rebel. The lords decided to increasingly move the samurai out of their lands in the countryside and force them to reside and work as bureaucrats in the castle-town, where it was far easier to control. By the same logic, the Edo Bakufu forced all the lords to alternate each year between living in Edo and their own domain, and all their immediate families were forced to reside in Edo to tie them to the Bakufu (and, of course, as hostages). The same arrangement applied to the highest ranking samurai of each domain, and naturally many lower ranking ones also travelled and lived with their lord in Edo to serve them. Being called up to follow the lord to Edo was considered a great honour, time spent in proximity to the lord may open up avenue of advancement, and there was of course the attraction of living in a big city with its many different goods and entertainment. This means that despite the high cost of living of a big city, as well as the cost of making the trip one-way each year, many samurai were more than happy to go. As described here, many domains spent well over half of their annual income on this arrangement.

This meant of course, samurai and their money from all over Japan were concentrated in Edo. Where there's money, people and goods naturally followed. Food from all along the Kanto Plain were carted into Edo, and ships carrying things from a lot further out pulled into ports at Kanda and Nihonbashi every day also brought food and goods into the city. Commoners, not just artisans but also people like restaurateurs, entertainers, the common noodle peddler, farm labourers in the off season or just poor migrant labourers, all flooded into Edo looking for opportunity. So, like other pre-industrial cities that reached this size in history, Edo was sustained by concentrating the resources of Japan into one city. Even then, there were signs the Edo government was having problems sustaining this large city, with constant attempts throughout this period to regulate the price of rice in Edo that was never permanently successful, and by the 18th century there were even (also unsuccessful) attempts to restrict migrant workers from flooding into the city and talks of returning people to the countryside.