Later on it will be no problem. Well, almost. When there are long strings of hiragana, if you don't know the vocabulary, it can be kind of hard to figure out how to pronounce things (at first glance at least). But once text starts having kanji, the は for particles and the は as pronounced normally are pretty apparent.
For example:
私はCharles Barkleyです。
スイカは好きだけど、オレンジは嫌いだ。
I like watermelon but I hate oranges.
今日は何時に勉強しはじめるの?
When will you start studying today?
はじめまして。
In the first two, the は are wa's, or particles. Often they come after nouns, or other particles such as に で etc. Since almost all nouns are either written in kanji or katakana, it's pretty apparent that what follows them is the particle wa.
In the last two, the last sentence, hajimemashite, ha is the first character in the sentence, so it obviously has to be pronounced ha. The other one might be a bit confusing: shiHAjimeru. You take the masu form of a verb, drop masu, add hajimeru, and you get 'to begin to do ~'. In this case, you see that the shi before the は is not in kanji, an is after benkyou, so it must be the beginning of an inflected verb. Particles will not break up an inflected verb, so you know it cant be prounced wa, and with enough familiarity, you'll quickly recognize the grammar point. Anyway, just gaman and keep reading and it won't be a problem anymore.
ETA: Others may have other opinions, but I think its best not to think of Japanese in terms of 'words.' More useful is thinking of things as nouns, particles, verbs, a long inflected string consisting of a verb + an ending, etc. Even more useful, and what I do now, is to kind of think of things as units, which are broken up by important partices. In the above examples:
今日は何時に勉強しはじめるの? I would break this up into 3 parts:
kyouwa nanjini benkyoushihajimeruno?
Thinking about it this way is quite helpful for pronounciation and for forming sentences, especially when speaking. You get through one part, then think of what the next part will be. It creates a more natural rhythm, which will obviously be slow and choppy at first, but will eventually get you there.