My city has a water shortage, fire stations needed, sewage overload and the need for transport and education. The only way I know to make money is from upgrading houses and selling stuff on the trade market. How else do I earn a lot of money?
There are several ways you can make money:
(1) Build or upgrade new residential buildings. Be careful to include new residential buildings within your existing service zones so that you don't have to worry about needing too many new services.
(2) Collect taxes on the residential buildings that you have. This is much slower than other ways to make money, but over time, if your sims are happy, will provide a good, steady payout.
(3) Trade items on the global exchange. Really good rates go for items that are needed to expand city storage (ladders, security cameras, padlock), to expand map areas (dozer exhaust, plow, gear), and for doing disaster events (gloves, buttons, batteries). However, you can sell ANYTHING that you manufacture or create in a factory on the global exchange.
(4) Wait for simoleon bubbles to pop up and complete the trade that's asked for. Many times it will be for manufactured goods, but sometimes they ask for expansion items. If you don't have the items right now, you can manufacture the goods and go back to the bubble later and sell the items when you've completed the manufacturing.
(5) Do cargo shipments on either the boat or the airport. By fulfilling those items not only do you receive simoleons but also keys and other items to purchase specialized services that are unlocked later on in the game.
Also, in general, it pays off in the long run to purchase the most expensive police stations, hospitals and fire stations to encompass the largest area. Also, it makes sense to invest in better sewage, water and power options. Then you don't have to worry as much about making sure you're covered.
Try and focus on upgrading houses to the max (or close) before building more, as a 2000+ citizens apartment building is equivalent in needs to a 20-citizen house, but earns you much more money in taxes. Slowly build your city from a cluster of buildings, adding a couple every time you max the older ones out, and you'll level up steadily with 100% satisfaction.
Note that specialisation needs are not as severe as utility/park needs; citizens won't leave due to lack of schools but they will leave due to lack of water.
Also, invest in cargo shipments when you can because they earn you some coins and keys (which are later immensely useful for specialisation buildings).
When I really needed money I also sold some area & storage expansion items, since they're worth quite a lot but come relatively often. (And I didn't need them at the time)